Underwater Domains in Yellowstone Lake Hydrothermal Vent Geochemistry and Bacterial Chemosynthesis
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Marsarchaeota Are an Aerobic Archaeal Lineage Abundant in Geothermal Iron Oxide Microbial Mats
Marsarchaeota are an aerobic archaeal lineage abundant in geothermal iron oxide microbial mats Authors: Zackary J. Jay, Jacob P. Beam, Mansur Dlakic, Douglas B. Rusch, Mark A. Kozubal, and William P. Inskeep This is a postprint of an article that originally appeared in Nature Microbiology on May 14, 2018. The final version can be found at https://dx.doi.org/10.1038/s41564-018-0163-1. Jay, Zackary J. , Jacob P. Beam, Mensur Dlakic, Douglas B. Rusch, Mark A. Kozubal, and William P. Inskeep. "Marsarchaeota are an aerobic archaeal lineage abundant in geothermal iron oxide microbial mats." Nature Microbiology 3, no. 6 (May 2018): 732-740. DOI: 10.1038/ s41564-018-0163-1. Made available through Montana State University’s ScholarWorks scholarworks.montana.edu Marsarchaeota are an aerobic archaeal lineage abundant in geothermal iron oxide microbial mats Zackary J. Jay1,4,7, Jacob P. Beam1,5,7, Mensur Dlakić2, Douglas B. Rusch3, Mark A. Kozubal1,6 and William P. Inskeep 1* The discovery of archaeal lineages is critical to our understanding of the universal tree of life and evolutionary history of the Earth. Geochemically diverse thermal environments in Yellowstone National Park provide unprecedented opportunities for studying archaea in habitats that may represent analogues of early Earth. Here, we report the discovery and character- ization of a phylum-level archaeal lineage proposed and herein referred to as the ‘Marsarchaeota’, after the red planet. The Marsarchaeota contains at least two major subgroups prevalent in acidic, microaerobic geothermal Fe(III) oxide microbial mats across a temperature range from ~50–80 °C. Metagenomics, single-cell sequencing, enrichment culturing and in situ transcrip- tional analyses reveal their biogeochemical role as facultative aerobic chemoorganotrophs that may also mediate the reduction of Fe(III). -
Life at Acidic Ph Imposes an Increased Energetic Cost for a Eukaryotic Acidophile Mark A
CORE Metadata, citation and similar papers at core.ac.uk Provided by e-Prints Soton The Journal of Experimental Biology 208, 2569-2579 2569 Published by The Company of Biologists 2005 doi:10.1242/jeb.01660 Life at acidic pH imposes an increased energetic cost for a eukaryotic acidophile Mark A. Messerli1,2,*, Linda A. Amaral-Zettler1, Erik Zettler3,4, Sung-Kwon Jung2, Peter J. S. Smith2 and Mitchell L. Sogin1 1The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA, 2BioCurrents Research Center, Program in Molecular Physiology, Marine Biological Laboratory, Woods Hole, MA 02543, USA, 3Sea Education Association, PO Box 6, Woods Hole, MA 02543, USA and 4Centro de Biología Molecular, Universidad Autónoma de Madrid, Cantoblanco, Madrid 28049, Spain *Author for correspondence (e-mail: [email protected]) Accepted 25 April 2005 Summary Organisms growing in acidic environments, pH·<3, potential difference of Chlamydomonas sp., measured would be expected to possess fundamentally different using intracellular electrodes at both pH·2 and 7, is close molecular structures and physiological controls in to 0·mV, a rare value for plants, animals and protists. The comparison with similar species restricted to neutral pH. 40·000-fold difference in [H+] could be the result of either We begin to investigate this premise by determining the active or passive mechanisms. Evidence for active magnitude of the transmembrane electrochemical H+ maintenance was detected by monitoring the rate of ATP gradient in an acidophilic Chlamydomonas sp. (ATCC® consumption. At the peak, cells consume about 7% more PRA-125) isolated from the Rio Tinto, a heavy metal ATP per second in medium at pH·2 than at pH·7. -
Phylogenetics of Archaeal Lipids Amy Kelly 9/27/2006 Outline
Phylogenetics of Archaeal Lipids Amy Kelly 9/27/2006 Outline • Phlogenetics of Archaea • Phlogenetics of archaeal lipids • Papers Phyla • Two? main phyla – Euryarchaeota • Methanogens • Extreme halophiles • Extreme thermophiles • Sulfate-reducing – Crenarchaeota • Extreme thermophiles – Korarchaeota? • Hyperthermophiles • indicated only by environmental DNA sequences – Nanoarchaeum? • N. equitans a fast evolving euryarchaeal lineage, not novel, early diverging archaeal phylum – Ancient archael group? • In deepest brances of Crenarchaea? Euryarchaea? Archaeal Lipids • Methanogens – Di- and tetra-ethers of glycerol and isoprenoid alcohols – Core mostly archaeol or caldarchaeol – Core sometimes sn-2- or Images removed due to sn-3-hydroxyarchaeol or copyright considerations. macrocyclic archaeol –PMI • Halophiles – Similar to methanogens – Exclusively synthesize bacterioruberin • Marine Crenarchaea Depositional Archaeal Lipids Biological Origin Environment Crocetane methanotrophs? methane seeps? methanogens, PMI (2,6,10,15,19-pentamethylicosane) methanotrophs hypersaline, anoxic Squalane hypersaline? C31-C40 head-to-head isoprenoids Smit & Mushegian • “Lost” enzymes of MVA pathway must exist – Phosphomevalonate kinase (PMK) – Diphosphomevalonate decarboxylase – Isopentenyl diphosphate isomerase (IPPI) Kaneda et al. 2001 Rohdich et al. 2001 Boucher et al. • Isoprenoid biosynthesis of archaea evolved through a combination of processes – Co-option of ancestral enzymes – Modification of enzymatic specificity – Orthologous and non-orthologous gene -
Analysis of a Multicomponent Thermostable DNA Polymerase III Replicase from an Extreme Thermophile*
THE JOURNAL OF BIOLOGICAL CHEMISTRY Vol. 277, No. 19, Issue of May 10, pp. 17334–17348, 2002 © 2002 by The American Society for Biochemistry and Molecular Biology, Inc. Printed in U.S.A. Analysis of a Multicomponent Thermostable DNA Polymerase III Replicase from an Extreme Thermophile* Received for publication, October 23, 2001, and in revised form, February 18, 2002 Published, JBC Papers in Press, February 21, 2002, DOI 10.1074/jbc.M110198200 Irina Bruck‡, Alexander Yuzhakov§¶, Olga Yurieva§, David Jeruzalmi§, Maija Skangalis‡§, John Kuriyan‡§, and Mike O’Donnell‡§ʈ From §The Rockefeller University and ‡Howard Hughes Medical Institute, New York, New York 10021 This report takes a proteomic/genomic approach to polymerase III (pol III) structure and function has been ob- characterize the DNA polymerase III replication appa- tained from studies of the Escherichia coli replicase, DNA ratus of the extreme thermophile, Aquifex aeolicus. polymerase III holoenzyme (reviewed in Ref. 6). Therefore, a Genes (dnaX, holA, and holB) encoding the subunits re- brief overview of its structure and function is instructive for the ␦ ␦ quired for clamp loading activity ( , , and ) were iden- comparisons to be made in this report. In E. coli, the catalytic Downloaded from tified. The dnaX gene produces only the full-length subunit of DNA polymerase III is the ␣ subunit (129.9 kDa) product, , and therefore differs from Escherichia coli encoded by dnaE; it lacks a proofreading exonuclease (7). The dnaX that produces two proteins (␥ and ). Nonetheless, Ј Ј ⑀ ␦␦ proofreading 3 –5 -exonuclease activity is contained in the the A. aeolicus proteins form a complex. The dnaN ␣ ,␦␦ (27.5 kDa) subunit (dnaQ) that forms a 1:1 complex with (8  gene encoding the clamp was identified, and the ␣Ϫ⑀  9). -
Functionalized Membrane Domains: an Ancestral Feature of Archaea? Maxime Tourte, Philippe Schaeffer, Vincent Grossi, Phil Oger
Functionalized Membrane Domains: An Ancestral Feature of Archaea? Maxime Tourte, Philippe Schaeffer, Vincent Grossi, Phil Oger To cite this version: Maxime Tourte, Philippe Schaeffer, Vincent Grossi, Phil Oger. Functionalized Membrane Domains: An Ancestral Feature of Archaea?. Frontiers in Microbiology, Frontiers Media, 2020, 11, pp.526. 10.3389/fmicb.2020.00526. hal-02553764 HAL Id: hal-02553764 https://hal.archives-ouvertes.fr/hal-02553764 Submitted on 20 May 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. fmicb-11-00526 March 30, 2020 Time: 21:44 # 1 ORIGINAL RESEARCH published: 31 March 2020 doi: 10.3389/fmicb.2020.00526 Functionalized Membrane Domains: An Ancestral Feature of Archaea? Maxime Tourte1†, Philippe Schaeffer2†, Vincent Grossi3† and Phil M. Oger1*† 1 Université de Lyon, INSA Lyon, CNRS, MAP UMR 5240, Villeurbanne, France, 2 Université de Strasbourg-CNRS, UMR 7177, Laboratoire de Biogéochimie Moléculaire, Strasbourg, France, 3 Université de Lyon, ENS Lyon, CNRS, Laboratoire de Géologie de Lyon, UMR 5276, Villeurbanne, France Bacteria and Eukarya organize their plasma membrane spatially into domains of distinct functions. Due to the uniqueness of their lipids, membrane functionalization in Archaea remains a debated area. -
Thermophilic Carboxydotrophs and Their Applications in Biotechnology Springerbriefs in Microbiology
SPRINGER BRIEFS IN MICROBIOLOGY EXTREMOPHILIC BACTERIA Sonia M. Tiquia-Arashiro Thermophilic Carboxydotrophs and their Applications in Biotechnology SpringerBriefs in Microbiology Extremophilic Bacteria Series editors Sonia M. Tiquia-Arashiro, Dearborn, MI, USA Melanie Mormile, Rolla, MO, USA More information about this series at http://www.springer.com/series/11917 Sonia M. Tiquia-Arashiro Thermophilic Carboxydotrophs and their Applications in Biotechnology 123 Sonia M. Tiquia-Arashiro Department of Natural Sciences University of Michigan Dearborn, MI USA ISSN 2191-5385 ISSN 2191-5393 (electronic) ISBN 978-3-319-11872-7 ISBN 978-3-319-11873-4 (eBook) DOI 10.1007/978-3-319-11873-4 Library of Congress Control Number: 2014951696 Springer Cham Heidelberg New York Dordrecht London © The Author(s) 2014 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. Exempted from this legal reservation are brief excerpts in connection with reviews or scholarly analysis or material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. Duplication of this publication or parts thereof is permitted only under the provisions of the Copyright Law of the Publisher’s location, in its current version, and permission for use must always be obtained from Springer. -
EXTREMOPHILES – Vol
EXTREMOPHILES – Vol. I - Extremophiles: Basic Concepts - Charles Gerday EXTREMOPHILES: BASIC CONCEPTS Charles Gerday Laboratory of Biochemistry, University of Liège, Belgium Keywords: extremophiles, thermophiles, halophiles, alkaliphiles, acidophiles, metallophiles, barophiles, psychrophiles, piezophiles, extreme conditions Contents 1. Introduction 2. Effects of Extreme Conditions on Cellular Components 2.1. Membrane Structure 2.2. Nucleic Acids 2.2.1. Introduction 2.2.2. Desoxyribonucleic Acids 2.2.3. Ribonucleic Acids 2.3. Proteins 2.3.1. Introduction 2.3.2. Thermophilic Proteins 2.3.3. Psychrophilic Proteins 2.3.4. Halophilic Proteins 2.3.5. Piezophilic Proteins 2.3.6. Alkaliphilic Proteins 2.3.7. Acidophilic Proteins 3. Conclusions Acknowledgments Glossary Bibliography Biographical Sketch Summary Extremophiles are organisms which permanently experience environmental conditions which mayUNESCO be considered as extreme –in comparisonEOLSS to the physico-chemical characteristics of the normal environment of human cells: the latter belonging to the mesophile or temperate world. Some eukaryotic organisms such as fishes, invertebrates, yeasts, fungi, and plants have partially colonized extreme habitats characterized by low temperature and/orSAMPLE of elevated hydrostatic pressure. CHAPTERS In general, however, the organisms capable of thriving at the limits of temperature, pH, salt concentration and hydrostatic pressure, are prokaryotic. In fact, some organisms depend on these extreme conditions for survival and have therefore developed unique adaptations, especially at the level of their membranes and macromolecules, and affecting proteins and nucleic acids in particular. The molecular bases of the various adaptations are beginning to be understood and are briefly described. The study of the extremophile world has contributed greatly to defining, in more precise terms, fundamental concepts such as macromolecule stability and protein folding. -
Deep-Sea Hydrothermal Vent Euryarchaeota 2”
View metadata, citation and similar papers at core.ac.uk brought to you by CORE ORIGINAL RESEARCH ARTICLE published: 20 February 2012provided by PubMed Central doi: 10.3389/fmicb.2012.00047 Distribution, abundance, and diversity patterns of the thermoacidophilic “deep-sea hydrothermal vent euryarchaeota 2” Gilberto E. Flores†, Isaac D. Wagner,Yitai Liu and Anna-Louise Reysenbach* Department of Biology, Center for Life in Extreme Environments, Portland State University, Portland, OR, USA Edited by: Cultivation-independent studies have shown that taxa belonging to the “deep-sea Kirsten Silvia Habicht, University of hydrothermal vent euryarchaeota 2” (DHVE2) lineage are widespread at deep-sea Southern Denmark, Denmark hydrothermal vents. While this lineage appears to be a common and important mem- Reviewed by: Kuk-Jeong Chin, Georgia State ber of the microbial community at vent environments, relatively little is known about their University, USA overall distribution and phylogenetic diversity. In this study, we examined the distribu- Elizaveta Bonch-Osmolovskyaya, tion, relative abundance, co-occurrence patterns, and phylogenetic diversity of cultivable Winogradsky Institute of Microbiology thermoacidophilic DHVE2 in deposits from globally distributed vent fields. Results of quan- Russian Academy of Sciences, Russia titative polymerase chain reaction assays with primers specific for the DHVE2 and Archaea *Correspondence: Anna-Louise Reysenbach, demonstrate the ubiquity of the DHVE2 at deep-sea vents and suggest that they are sig- Department of Biology, Center for nificant members of the archaeal communities of established vent deposit communities. Life in Extreme Environments, Local similarity analysis of pyrosequencing data revealed that the distribution of the DHVE2 Portland State University, PO Box was positively correlated with 10 other Euryarchaeota phylotypes and negatively correlated 751, Portland, OR 97207-0751, USA. -
Discovery of Chemosynthesis-Based Association on the Cretaceous Basal Leatherback Sea Turtle from Japan
Editors' choice Discovery of chemosynthesis-based association on the Cretaceous basal leatherback sea turtle from Japan ROBERT G. JENKINS, ANDRZEJ KAIM, KEI SATO, KAZUHIRO MORIYA, YOSHINORI HIKIDA, and REN HIRAYAMA Jenkins, R.G., Kaim, A., Sato, K., Moriya, K., Hikida, Y., and Hirayama, R. 2017. Discovery of chemosynthesis-based association on the Cretaceous basal leatherback sea turtle from Japan. Acta Palaeontologica Polonica 62 (4): 683–690. We report a Late Cretaceous chemosynthetic community fueled by decomposing basal leatherback sea turtle on the ocean floor in the western Pacific. The fossil association representing this community has been recovered from the matrix of a concretion containing a single carapace of Mesodermochelys sp. from Late Cretaceous outer shelf to upper slope deposit of northern Hokkaido, Japan. The carapace displays boreholes most likely performed by boring bivalves, and is associated with molluscan shells, mainly Provanna cf. nakagawensis and Thyasira tanabei. Since this association is similar to fauna already known from Late Cretaceous hydrocarbon seeps, sunken wood, and plesiosaur-falls in Hokkaido, it is suggested that all types of chemosynthesis-based communities in the Late Cretaceous of western Pacific may have belonged to the same regional pool of animals and were not yet fully differentiated into three independent types of com- munities as it is known today. This finding also indicates that the sulfophilic stage of the vertebrate-fall communities was supported not only by plesiosaur carcasses, which were previously reported, but also by sea turtle carcasses. It highlights the possibility of surviving vertebrate-fall communities through the end-Cretaceous mass extinction event on carcasses of sea turtles which are the only large marine vertebrates surviving this event. -
Chapter 5 Hmdscience.Com EN Online Vir Onmental Science Work Ecosystems How
DO NOT EDIT--Changes must be made through “File info” printcode=a Chapter 5 Section 1 Energy Flow in Ecosystems How Section 2 The Cycling of Matter Section 3 How Ecosystems Change Why It Matters Ecosystems This frog gets the energy it needs to survive by eating other organisms, such as damselflies. Frogs and damselflies are both consumers in an aquatic food chain. Work How does energy continue to be transferred in this food chain? CASESTUDY Learn how pollutants, like the pesticide DDT, are transferred through a food chain in the case study DDT in an Aquatic Food Chain on page 120. Online enVirOnmental Science HMDScience.com Go online to access additional resources, including labs, worksheets, multimedia, and resources in Spanish. Inc. Cosmos Blank/Photo Researchers, ©A. 116 DO NOT EDIT--Changes must be made through “File info” printcode=a Section 1 Energy Flow in Objectives Describe how energy is transferred from the sun Ecosystems to producers and then to consumers. organisms need energy to survive, grow, and reproduce. Different organisms Describe one way in which get energy from different sources, but the ultimate source of energy for almost all consumers depend on producers. organisms on earth is the sun. Identify two types of consumers. Explain how energy transfer in a Life Depends on the Sun food web is more complex than Energy from the sun enters an ecosystem when organisms use sunlight energy transfer in a food chain. to make sugar in a process called photosynthesis. During photosynthesis, plants, algae, and some bacteria capture light energy from the sun and Explain why an energy pyramid use it to convert carbon dioxide and water into sugar and oxygen, as is a representation of trophic shown in Figure 1.1. -
Life in Extreme Heat
THERMOPHILES Thermophiles, or heat-loving microscopic organisms, are nourished by the extreme habitat at hydrothermal features in Yellowstone National Park. They also color hydrothermal features shown here at Clepsydra Geyser. Life in Extreme Heat The hydrothermal features of Yellowstone are enough to blister your skin. Some create layers that magnificent evidence of Earth’s volcanic activity. look like molten wax on the surface of steaming Amazingly, they are also habitats in which micro- alkaline pools. Still others, apparent to us through scopic organisms called thermophiles—“thermo” for the odors they create, exist only in murky, sulfuric heat, “phile” for lover—survive and thrive. caldrons that stink worse than rotten eggs. Grand Prismatic Spring at Midway Geyser Basin Today, many scientists study Yellowstone’s ther- is an outstanding example of this dual characteristic. mophiles. Some of these microbes are similar to the Visitors marvel at its size and brilliant colors. The boardwalk crosses a vast habitat for thermophiles. Nourished by energy and chemical building blocks Words to Know available in the hot springs, microbes construct Extremophile: A microorganism living in extreme vividly colored communities. Living with these conditions such as heat and acid, that cannot survive without these conditions. microscopic life forms are larger examples of life in extreme environments, such as mites, flies, spiders, Thermophile: Heat-loving extremophile. and plants. Microorganism: Single- or multi-celled organism of microscopic or submicroscopic size. Also called a microbe. For thousands of years, people have likely won- dered about these extreme habitats. The color of Microbes in Yellowstone: In addition to the thermophilic microorganisms, millions of other microbes thrive in Yellowstone’s superheated environments certainly Yellowstone’s soils, streams, rivers, lakes, vegetation, and caused geologist Walter Harvey Weed to pause, think, animals. -
A Brief Journey to the Microbial World
2 A Brief Journey to the Microbial World Green sulfur bacteria are I Seeing the Very Small 25 phototrophic microorganisms 2.1 Some Principles of Light Microscopy 25 that form their own phyloge- 2.2 Improving Contrast in Light Microscopy 26 netic lineage and were some 2.3 Imaging Cells in Three Dimensions 29 of the first phototrophs to 2.4 Electron Microscopy 30 evolve on Earth. II Cell Structure and Evolutionary History 31 2.5 Elements of Microbial Structure 31 2.6 Arrangement of DNA in Microbial Cells 33 2.7 The Evolutionary Tree of Life 34 III Microbial Diversity 36 2.8 Metabolic Diversity 36 2.9 Bacteria 38 2.10 Archaea 41 2.11 Phylogenetic Analyses of Natural Microbial Communities 43 2.12 Microbial Eukarya 43 CHAPTER 2 • A Brief Journey to the Microbial World 25 for which resolution is considerably greater than that of the light I Seeing the Very Small microscope. UNIT 1 istorically, the science of microbiology blossomed as the The Compound Light Microscope ability to see microorganisms improved; thus, microbiology H The light microscope uses visible light to illuminate cell struc- and microscopy advanced hand-in-hand. The microscope is the tures. Several types of light microscopes are used in microbiol- microbiologist’s most basic tool, and every student of microbiol- ogy: bright-field, phase-contrast, differential interference contrast, ogy needs some background on how microscopes work and how dark-field, and fluorescence. microscopy is done. We therefore begin our brief journey to the With the bright-field microscope, specimens are visualized microbial world by considering different types of microscopes because of the slight differences in contrast that exist between and the applications of microscopy to imaging microorganisms.